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Hanusová, L., A. Míková, L. Večerek, D. Schroeffelová, V. Řehout, L. Tothová, K. Vernerová, B. Hosnedlová, and J. Čítek. "Effect of DGAT1 polymorphisms on the estimated breeding values of Czech Simmental sires." Czech Journal of Animal Science 59, No. 8 (August 26, 2014): 365–73. http://dx.doi.org/10.17221/7587-cjas.
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The aim was to evaluate the effect of polymorphisms in the promoter and in the coding region of the DGAT1 gene on the estimated breeding values (EBV) of Czech Simmental sires. The K232A polymorphism (n = 191) in the coding region was genotyped by PCR/RFLP, and the KU and SA polymorphisms in the promoter (n = 203) were identified in an automatic sequencer. In the K232A polymorphism, the frequency of the genotype AA (Alanine) was greater than that of the genotype KA, the homozygous genotype KK (Lysine) was not found. Similarly, the allele A predominated over the K allele (0.945 and 0.055). The EBV for milk performance have been assigned to the genotypes, and the associations quantified. For the AA genotype and A allele, positive association with EBV of milk yield and protein yield was found, and negative association with the breeding values of fat percentage and yield, and protein percentage, but only the value of fat content was found to be significant. The positive non-significant association of the A variant with the protein yield was caused by the high milk yield. In the KU polymorphism, the CC genotype was associated significantly with lower EBV for the fat percentage, both the C allele and the CC genotype were associated with higher EBV for milk yield, so both the fat and the protein yield were non-significantly increased. For the diplotypes K232A/KU, there was a significant association with the fat percentage. The AACC combination seemed to have some breeding potential. The K232A polymorphism explained maximum of 6.2% of EBV variability, the KU polymorphism of 4.4%, and the SA polymorphism of 4.2%. The diplotypes K232A/KU explained maximum of 7.4% of variability. The highest proportion of variability was explained for fat percentage. The results confirmed the important role of the BTA14 region in controlling milk performance.
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Karimi, Zahra, Brian Sullivan, and Mohsen Jafarikia. "45 A permutation test for validation of genomic estimated breeding values." Journal of Animal Science 98, Supplement_4 (November 3, 2020): 8–9. http://dx.doi.org/10.1093/jas/skaa278.016.
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Abstract Previous studies have shown that the accuracy of Genomic Estimated Breeding Value (GEBV) as a predictor of future performance is higher than the traditional Estimated Breeding Value (EBV). The purpose of this study was to estimate the potential advantage of selection on GEBV for litter size (LS) compared to selection on EBV in the Canadian swine dam line breeds. The study included 236 Landrace and 210 Yorkshire gilts born in 2017 which had their first farrowing after 2017. GEBV and EBV for LS were calculated with data that was available at the end of 2017 (GEBV2017 and EBV2017, respectively). De-regressed EBV for LS in July 2019 (dEBV2019) was used as an adjusted phenotype. The average dEBV2019 for the top 40% of sows based on GEBV2017 was compared to the average dEBV2019 for the top 40% of sows based on EBV2017. The standard error of the estimated difference for each breed was estimated by comparing the average dEBV2019 for repeated random samples of two sets of 40% of the gilts. In comparison to the top 40% ranked based on EBV2017, ranking based on GEBV2017 resulted in an extra 0.45 (±0.29) and 0.37 (±0.25) piglets born per litter in Landrace and Yorkshire replacement gilts, respectively. The estimated Type I errors of the GEBV2017 gain over EBV2017 were 6% and 7% in Landrace and Yorkshire, respectively. Considering selection of both replacement boars and replacement gilts using GEBV instead of EBV can translate into increased annual genetic gain of 0.3 extra piglets per litter, which would more than double the rate of gain observed from typical EBV based selection. The permutation test for validation used in this study appears effective with relatively small data sets and could be applied to other traits, other species and other prediction methods.
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Nwogwugwu, Chiemela Peter, Yeongkuk Kim, Yun Ji Chung, Sung Bong Jang, Seung Hee Roh, Sidong Kim, Jun Heon Lee, Tae Jeong Choi, and Seung-Hwan Lee. "Effect of errors in pedigree on the accuracy of estimated breeding value for carcass traits in Korean Hanwoo cattle." Asian-Australasian Journal of Animal Sciences 33, no. 7 (July 1, 2020): 1057–67. http://dx.doi.org/10.5713/ajas.19.0021.
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Objective: This study evaluated the effect of pedigree errors (PEs) on the accuracy of estimated breeding value (EBV) and genetic gain for carcass traits in Korean Hanwoo cattle.Methods: The raw data set was based on the pedigree records of Korean Hanwoo cattle. The animals’ information was obtained using Hanwoo registration records from Korean animal improvement association database. The record comprised of 46,704 animals, where the number of the sires used was 1,298 and the dams were 38,366 animals. The traits considered were carcass weight (CWT), eye muscle area (EMA), back fat thickness (BFT), and marbling score (MS). Errors were introduced in the pedigree dataset through randomly assigning sires to all progenies. The error rates substituted were 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, and 80%, respectively. A simulation was performed to produce a population of 1,650 animals from the pedigree data. A restricted maximum likelihood based animal model was applied to estimate the EBV, accuracy of the EBV, expected genetic gain, variance components, and heritability (h2) estimates for carcass traits. Correlation of the simulated data under PEs was also estimated using Pearson’s method.Results: The results showed that the carcass traits per slaughter year were not consistent. The average CWT, EMA, BFT, and MS were 342.60 kg, 78.76 cm<sup>2, 8.63 mm, and 3.31, respectively. When errors were introduced in the pedigree, the accuracy of EBV, genetic gain and h2 of carcass traits was reduced in this study. In addition, the correlation of the simulation was slightly affected under PEs.Conclusion: This study reveals the effect of PEs on the accuracy of EBV and genetic parameters for carcass traits, which provides valuable information for further study in Korean Hanwoo cattle.
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Lee, Yun-Mi, Chang-Gwon Dang, Mohammad Z. Alam, You-Sam Kim, Kwang-Hyeon Cho, Kyung-Do Park, and Jong-Joo Kim. "The effectiveness of genomic selection for milk production traits of Holstein dairy cattle." Asian-Australasian Journal of Animal Sciences 33, no. 3 (March 1, 2020): 382–89. http://dx.doi.org/10.5713/ajas.19.0546.
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Objective: This study was conducted to test the efficiency of genomic selection for milk production traits in a Korean Holstein cattle population.Methods: A total of 506,481 milk production records from 293,855 animals (2,090 heads with single nucleotide polymorphism information) were used to estimate breeding value by single step best linear unbiased prediction.Results: The heritability estimates for milk, fat, and protein yields in the first parity were 0.28, 0.26, and 0.23, respectively. As the parity increased, the heritability decreased for all milk production traits. The estimated generation intervals of sire for the production of bulls (L<sub>SB</sub>) and that for the production of cows (L<sub>SC</sub>) were 7.9 and 8.1 years, respectively, and the estimated generation intervals of dams for the production of bulls (L<sub>DB</sub>) and cows (L<sub>DC</sub>) were 4.9 and 4.2 years, respectively. In the overall data set, the reliability of genomic estimated breeding value (GEBV) increased by 9% on average over that of estimated breeding value (EBV), and increased by 7% in cows with test records, about 4% in bulls with progeny records, and 13% in heifers without test records. The difference in the reliability between GEBV and EBV was especially significant for the data from young bulls, i.e. 17% on average for milk (39% vs 22%), fat (39% vs 22%), and protein (37% vs 22%) yields, respectively. When selected for the milk yield using GEBV, the genetic gain increased about 7.1% over the gain with the EBV in the cows with test records, and by 2.9% in bulls with progeny records, while the genetic gain increased by about 24.2% in heifers without test records and by 35% in young bulls without progeny records.Conclusion: More genetic gains can be expected through the use of GEBV than EBV, and genomic selection was more effective in the selection of young bulls and heifers without test records.
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KEMP, R. A., and J. W. WILTON. "THE EFFECT OF DIFFERENT NUMERATOR RELATIONSHIP MATRICES ON BREEDING VALUES ESTIMATED FROM MULTIPLE TRAIT BLUP." Canadian Journal of Animal Science 67, no. 1 (March 1, 1987): 201–4. http://dx.doi.org/10.4141/cjas87-022.
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A numerator relationship matrix (Ac) due to sires and dams was compared with a numerator relationship matrix (Ai) due to sires and maternal grandsires in a multiple-trait-reduced animal model (MT-RAM). Best linear unbiased predictors of estimated breeding values (EBV) for 200-d weight (WW) and postweaning gain (PG) (gain from 200 to 365 d of age) were estimated from data simulating a beef cattle population. As expected, mean EBV and bias (EBV-BV) for both traits were not significantly affected by different relationship matrices. The mean variances of EBV with Ac were larger than those with Ai for both traits. The mean EBV variances were closer to mean BV variances with Ac compared to Ai, which is consistent with increased precision of EBV. Product-moment correlations of EBV and BV (accuracy of prediction) were not equal (P < 0.01) for Ac compared to Ai with WW or PG. The EBV using Ac were more accurate than EBV using Ai. The increased precision and accuracy of EBV from a MT-RAM with Ac would result in greater genetic progress in the population. Key words: Relationship matrices, estimated breeding values, MT-RAM
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Sender, G., K. G. A. Hameid, A. Korwin-Kossakowska, and M. Sobczynska. "Association of the <i>BoLA-DRB3</i> alleles with estimated breeding value for somatic cell count in Polish dairy cattle." Archives Animal Breeding 51, no. 2 (October 10, 2008): 111–19. http://dx.doi.org/10.5194/aab-51-111-2008.
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Abstract. Introducing resistance to mastitis into breeding programmes for dairy cattle seems to be one of the possible methods for limiting the increasing number of mastitis cases. Looking for candidate genes for genetic markers is one of the strategies. The BoLA–DRB3 alleles have considerable promise as potential mastitis marker. The objective of the study was to evaluate relationships between two BoLA–DRB3 alleles (BoLA–DRB3.2*16 and BoLA-DRB3.2*23) and estimated breeding value (EBV) for somatic cell count (SCC) in Polish dairy cattle. A total of 525 Polish Holstein cows in two experimental farms were evaluated for test-day SCC. The polymorphism of BoLA–DRB3 gene was identified using the MPT-PCR method. The variance components for test-day SCC were estimated by the REML method using animal model. The breeding value of SCC was calculated according to the BLUP method. Linear contrast between model-adjusted breeding values of SCC for all animals was used to test for differences between genotypes. In Polish Holstein cows population BoLA allele DRB3.2*23 was associated with increase of EBV for SCC in milk. It was observed increase of EBV for SCC from cows carrying this allele comparing to cows carrying BoLA–DRB3.2*16 (p ≤0.07) or other alleles (p ≤0.01).
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Bentley, Kelsey, Andrew R. Weaver, Joan M. Burke, Jim Morgan, Lee Wright, Scott P. Greiner, and Scott A. Bowdridge. "158 The effect of sire fecal egg count estimated breeding value on antibody production of grazing Katahdin lambs." Journal of Animal Science 98, Supplement_2 (November 1, 2020): 70. http://dx.doi.org/10.1093/jas/skz397.163.
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Abstract Over the past two years of mating high (Hi) or low (Lo) fecal egg count (FEC) EBV Katahdin rams randomly mated to Katahdin ewes, reduced FEC in lambs has been the hallmark trait observable at weaning. Upon additional analysis, death loss in lambs also segregated with sire FEC EBV; whereas, HiFEC-sired lambs had a death loss of 29.9% in 2018 and 14.5% in 2019. Yet, LoFEC-sired lambs had a death loss of 10% in both years. Increased death loss in 2018 may have been due to an outbreak of Clostridium perfringens Type-A and as a result lambs in 2019 were vaccinated for Clostridium type A. Regardless, this had no impact on death loss in LoFEC-sired lambs. Therefore, it can be hypothesized that sire FEC EBV indirectly selects for enhanced, generalized immunity. To initially test this hypothesis, serum was collected from HiFEC- and LoFEC-sired lambs weekly, prior to and after typical clostridium toxoid vaccination and boostering. Lamb serum was pooled by week and within sire, where there were 4 sires per FEC EBV group. Serum was analyzed for total immunoglobulin-G (IgG) by using absorbance at 450nm as the metric. Data were analyzed by using the general linear model of SAS with fixed effects of sire EBV type and week. A comparison of means was conducted by using the LS means procedure with Bonferroni adjustment. Absorbance of serum from LoFEC-sired lambs was higher across all time points than that of serum from HiFEC-sired lambs (1.66 vs. 1.41 ± 0.04; P < 0.0001), meaning that LoFEC-sired lambs had higher circulating IgG than lambs sired by HiFEC rams. Taken together, these data provide preliminary evidence that indicate segregation of lamb generalized immunity by sire FEC EBV.
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Udeh, I. "Estimation of breeding value for bodyweight of grasscutters." Nigerian Journal of Animal Production 48, no. 2 (March 2, 2021): 1–5. http://dx.doi.org/10.51791/njap.v48i2.2934.
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Animal breeders are interested in the genetic worth or total genetic merit of an animal for a given trait. The value of an animal in a breeding program for a particular trait is called the breeding value. The aim of this study was to predict the breeding values for bodyweight of grasscutters at 4, 6 and 8 months of age using univariate animal model. Four families of grasscutters with five grasscutters per family were used for the study. Families 3 and 4 had higher bodyweight at 4 and 6 months compared with families 1 and 2. Family 4 had the highest bodyweight at 8 month and family 2 had the least. The estimated breeding values (EBV) for bodyweight of grasscutters ranged from -0.06kg to 0.45kg at 4 month, -0.05kg to 0.45 kg at 6 month and -0.04kg to 0.55kg at 8 month. The reliability of the EBV (%) ranged from 51.00 to 62.50, 22.25 to 43.81 and 25.84 to 49.00 at 4, 6 and 8 months of age respectively. This implies that the correlations between estimated breeding value and true genetic merit were medium to high in magnitude. The reliability of the EBV could be improved further through collecting more phenotypic information on the animal and its relatives and by improving the heritability of the trait. Les éleveurs s'intéressent à la valeur génétique ou au mérite génétique total d'un animal pour un trait donné. La valeur d'un animal dans un programme d'élevage pour un trait particulier est appelée valeur de reproduction. Le but de cette étude était de prédire les valeurs de reproduction du poids corporel des coupe-herbes à l'âge de 4, 6 et 8 mois à l'aide d'un modèle animal univarié. Quatre familles de coupe-herbes avec cinq coupes-herbes par famille ont été utilisées pour l'étude. Les familles 3 et 4 avaient un poids corporel plus élevé à 4 et 6 mois comparativement aux familles 1 et 2. Famille 4 avait le poids corporel le plus élevé à 8 mois et la famille 2 avait le moins. Les valeurs de reproduction estimées (le 'EBV') pour le poids corporel des coupe-herbes allaient de -0.06 kg à 0,45 kg à 4 mois, -0.05 kg à 0.45 kg à 6 mois et -0.04 kg à 0.55 kg à 8 mois. La fiabilité de l'EBV (%) 51.00 à 62.50, 22.25 à 43.81 et 25.84 à 49.00 à 4, 6 et 8 mois respectivement. Cela implique que les corrélations entre la valeur de reproduction estimée et le véritable mérite génétique étaient de taille moyenne à élevée. La fiabilité de l'EBV pourrait être encore améliorée en recueillant plus d'informations phénotypique sur l'animal et ses parents et en améliorant l'hérabilité du trait.
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Uimari, Pekka, and Esa A. Mäntysaari. "Relationship between bull dam herd characteristics and bias in estimated breeding value of bull." Agricultural and Food Science 4, no. 5-6 (December 1, 1995): 463–72. http://dx.doi.org/10.23986/afsci.72622.
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The objective of the study was to relate estimated breeding values (EBVs) of the parents’ 305-days protein production and the bull dam herd-year characteristics to the empirical bias in pedigree indices (difference between the pedigree index and the final proof) of young bulls. Two animal model evaluations were carried out; one included records up to 1990 and the other up to spring 1992. The final data set included 242 bulls with pedigree indices, final proofs, parents’ EBVs, production and herd information (the size, the average production and the intraherd standard deviation) of the dams. The average empirical bias in pedigree indices was 13.6 kg. The correlation between the final proof of the bull and the EBVs of the bull sire or dam were 0.45 and 0.17, respectively. The low correlation with bull dam EBV indicates the unreliability of the bull dam EBVs. Size of the herd and the standard deviation of production in the herd when bull dam produced its third lactation were correlated with the empirical bias in pedigree index. Pedigree indices of the bulls coming from small herds with high intraherd standard deviation were more biased than those from the big herds with low intraherd standard deviation. The best bulls, when grouped according to their final proofs, were sons of the highest EBV sires. EBVs of bull dams did not differ in the highest and the lowest final proof groups, but the dams of the best bull group had a higher first lactation record than the dams of the other bull groups.
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Allingham, P. G., G. E. Gardner, M. Taylor, R. S. Hegarty, and G. S. Harper. "Effects of sire genotype and plane of nutrition on fascicular structure of M. longissimus thoracis et lumborum and its effect on eating quality." Australian Journal of Agricultural Research 57, no. 6 (2006): 641. http://dx.doi.org/10.1071/ar04319.
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The purpose of this study was to determine if estimated breeding value (EBV) of an animal’s sire and or the animal’s nutrition affected the structure of its M. longissimus thoracis et lumborum (LL) and, hence, the eating quality of meat derived from its carcass. Lambs were chosen based on the EBV of their sires in terms of post-weaning live weight (PWWT), post weaning fat at the C-site (PFAT), and post-weaning eye muscle depth (PEMD). Morphometric techniques were used to characterise muscle structure in terms of the distribution of intramuscular connective tissue; the variables together are called fascicular structure. Perimysial seam thickness and fascicular width were both influenced by sire estimated breeding values for PWWT, PFAT, and PEMD. Variation in fascicular structure was associated with an interaction between PEMD-EBV and PFAT-EBV of the sire. Fascicular width decreased with increased PEMD-EBV and increased with PFAT-EBV, but was not affected by PWWT-EBV. When the total seam thickness was adjusted to a common fascicular width, the lambs on a low plane of nutrition had relatively more intramuscular connective tissue than those on a high plane. The total seam thickness was negatively associated with PFAT-EBV and positively associated with PEMD-EBV. Warner Bratzler shear (WBS) peak force (PF) and initial yield were not associated with differences in sire EBV. The residual WBS shear force, peak force minus initial yield (PFIY), and compression values were negatively associated with nutrition but were positively associated with PWWT-EBV and PEMD-EBV of the sires. These latter 2 effects were moderated by nutrition. The data support the hypothesis that morphological characteristics of perimysium are genetically determined and nutritionally responsive. Variance in morphology accounted for some variance in the biophysical attributes of meat and may help explain why sheep with high muscling potential have tougher meat.
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Salvian, Mayara, Gerson Barreto Mourão, Gabriel Costa Monteiro Moreira, Mônica Corrêa Ledur, Luiz Lehmann Coutinho, and Matthew L. Spangler. "60 Re-ranking of estimated breeding values using different panel densities with ssGBLUP in broiler chickens." Journal of Animal Science 97, Supplement_2 (July 2019): 36–37. http://dx.doi.org/10.1093/jas/skz122.067.
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Abstract The aim of this study was to compare the rank of estimated breeding values (EBV) for organs (heart, liver, lungs and gizzard) and carcass (breast, thigh and drumstick) traits using pedigree-based BLUP (PBLUP) and single-step genomic BLUP (ssGBLUP) models. A total of 1,453 chickens (703 males and 750 females) from a paternal broiler (TT) reference population belonging to the Poultry Breeding Program from Embrapa Swine and Poultry were genotyped with the Axiom® Genome-Wide Chicken Genotyping Array (Affymetrix) 600K SNP panel. Samples with a call rate lower than 90% were removed. A SNP quality control was applied for removing SNP with call rate lower than 98%, MAF lower than 2% and significant deviations from HWE (p-value < 10–7) leaving 370,608 SNP for further analysis. Estimated breeding values were predicted using the blupf90 family of programs whereby a series of bi-variate animal models that included sex and hatching as fixed effects were fitted. Heritability estimates for carcass and organ traits obtained through PBLUP varied from low (0.16) for lungs to moderate (0.34 to 0.47) for heart, liver, gizzard, breast, thigh and drumstick. The genomic heritability estimates through ssGBLUP varied from low (0.14) for lungs to moderate (0.30 to .041) for all other traits. Five subsets (5, 10, 20, 40 and 80% of SNP) were randomly selected from the full SNP set to determine the impact, in terms of EBV rank, of using reduced subsets of SNP to inform relationships among individuals. Although the 5% subset of SNP consistently had the lowest correlation with the full set of SNP, all correlations were greater than 0.995. Results suggest that a relatively limited proportion of SNP could be used to reliably predict EBV via ssGBLUP in this population.
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Luan, Tu, John A. Woolliams, Sigbjørn Lien, Matthew Kent, Morten Svendsen, and Theo H. E. Meuwissen. "The Accuracy of Genomic Selection in Norwegian Red Cattle Assessed by Cross-Validation." Genetics 183, no. 3 (August 24, 2009): 1119–26. http://dx.doi.org/10.1534/genetics.109.107391.
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Genomic Selection (GS) is a newly developed tool for the estimation of breeding values for quantitative traits through the use of dense markers covering the whole genome. For a successful application of GS, accuracy of the prediction of genomewide breeding value (GW-EBV) is a key issue to consider. Here we investigated the accuracy and possible bias of GW-EBV prediction, using real bovine SNP genotyping (18,991 SNPs) and phenotypic data of 500 Norwegian Red bulls. The study was performed on milk yield, fat yield, protein yield, first lactation mastitis traits, and calving ease. Three methods, best linear unbiased prediction (G-BLUP), Bayesian statistics (BayesB), and a mixture model approach (MIXTURE), were used to estimate marker effects, and their accuracy and bias were estimated by using cross-validation. The accuracies of the GW-EBV prediction were found to vary widely between 0.12 and 0.62. G-BLUP gave overall the highest accuracy. We observed a strong relationship between the accuracy of the prediction and the heritability of the trait. GW-EBV prediction for production traits with high heritability achieved higher accuracy and also lower bias than health traits with low heritability. To achieve a similar accuracy for the health traits probably more records will be needed.
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Jalil, MA, S. Akther, MP Choudhury, and MA Habib. "Estimation of genetic parameters and prediction of breeding values for some economic traits of Black Bengal Goat under farming condition." Bangladesh Journal of Livestock Research 20, no. 1-2 (May 10, 2020): 8–17. http://dx.doi.org/10.3329/bjlr.v20i1-2.47013.
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The study was undertaken to evaluate the genetic progress of Black Bengal Goat (BBG) by estimating genetic parameters viz. heritability and breeding values for economically important productive and reproductive traits (birth weight, weight at 3, 6, 9 & 12 months, daily milk yield, lactation length, total milk yield and litter size of BBG goat population). Variance and co-variance components were analyzed applying Residual Maximum Likelihood (REML) approach by VCE 4.2.5 computer package. The heritability (h2) of birth weight was estimated as 0.2, which was low. The heritability estimates for 3-month weight (0.40), 6-month weight (0.50), 9-month weight (0.37) and 12-month weight (0.36) were found medium. Estimated h2 of daily milk yield, total milk yield and lactation length in this study were from 0.55 to 0.82. h2 of litter size was 0.09. The maximum estimated breeding value (EBV) was found for 6 month body weight (12.94 kg), however, for daily milk yield, the value was 1.513 kg. The results found in this study revealed that genetic improvement of BBG for most of the traits is possible by selection and breeding.
Bangladesh J. of Livestock Res. 20(1-2): 8-17, Jan-Dec 2013
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Putra, WPB, M. Sumadi, T. Hartatik, and H. Saumar. "Evaluation of growth traits of Aceh cattle at the breeding station in Indrapuri District of Indonesia." Bangladesh Journal of Animal Science 44, no. 2 (December 19, 2015): 85–91. http://dx.doi.org/10.3329/bjas.v44i2.26006.
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The present study was conducted using records on four breeding bulls maintained at the Indrapuris Breeding and Forages Center (IBFC) of Aceh Cattle, Indrapuri district, Indonesia and 52 of their progeny born from 2010 to 2014 through natural mating. Family selection was practiced in this breeding station. Traits included in this study were birth weight at 0 day (BWc), weaning weight at 205 days of age (WWc), yearling weight at 365 days of age (YWc) and final weight at 550 days of age (FWc) of their progeny. The variance and covariance components were estimated by the Paternal Half-sib Correlation method with the Excel sheets of Microsoft office computer program. The mean body weights of the animals were BWc (13.25+1.18 kg), WWc (47.80+10.00 kg), YWc (73.97+16.79 kg) and FWc (101.87+23.91 kg). Estimated heritability (h2) for BWC was low (h2 < 0.10) and the other traits were high (h2>0.30). Higher standard error (SE) value than h2 caused by less number of calves observation. Research showed that best relative accuracy value (RA>1.00) reached in BWC. but its trait was not effective as selection criterion because of lower h2 value. It was concluded that WWC could be used as selection criterion for breeding bulls based on the similar estimated breeding value (EBV) rank and high h2 value. The EBV of WWC from breeding bull ID: 0752 was calculated and ranked accordingly. The EBVs of three top bulls ID were 100412 (10.32 kg), 100520 (9.38 kg) and 100317 (6.75 kg) and three top heifers were 100526 (9.65 kg), 100408 (7.04 kg) and 100807 (5.20 kg). It can be concluded that these top ranking three bulls and heifers can be selected and used in the breeding programs.Bang. J. Anim. Sci. 2015. 44(2): 85-91
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Melnikova, Ekaterina, Artem Kabanov, Sergey Nikitin, Maria Somova, Sergey Kharitonov, Petr Otradnov, Olga Kostyunina, et al. "Application of Genomic Data for Reliability Improvement of Pig Breeding Value Estimates." Animals 11, no. 6 (May 27, 2021): 1557. http://dx.doi.org/10.3390/ani11061557.
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Replacement pigs’ genomic prediction for reproduction (total number and born alive piglets in the first parity), meat, fatness and growth traits (muscle depth, days to 100 kg and backfat thickness over 6–7 rib) was tested using single-step genomic best linear unbiased prediction ssGBLUP methodology. These traits were selected as the most economically significant and different in terms of heritability. The heritability for meat, fatness and growth traits varied from 0.17 to 0.39 and for reproduction traits from 0.12 to 0.14. We confirm from our data that ssGBLUP is the most appropriate method of genomic evaluation. The validation of genomic predictions was performed by calculating the correlation between preliminary GEBV (based on pedigree and genomic data only) with high reliable conventional estimates (EBV) (based on pedigree, own phenotype and offspring records) of validating animals. Validation datasets include 151 and 110 individuals for reproduction, meat and fattening traits, respectively. The level of correlation (r) between EBV and GEBV scores varied from +0.44 to +0.55 for meat and fatness traits, and from +0.75 to +0.77 for reproduction traits. Average breeding value (EBV) of group selected on genomic evaluation basis exceeded the group selected on parental average estimates by 22, 24 and 66% for muscle depth, days to 100 kg and backfat thickness over 6–7 rib, respectively. Prediction based on SNP markers data and parental estimates showed a significant increase in the reliability of low heritable reproduction traits (about 40%), which is equivalent to including information about 10 additional descendants for sows and 20 additional descendants for boars in the evaluation dataset.
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Shahinfar, Saleh, Hassan Mehrabani-Yeganeh, Caro Lucas, Ahmad Kalhor, Majid Kazemian, and Kent A. Weigel. "Prediction of Breeding Values for Dairy Cattle Using Artificial Neural Networks and Neuro-Fuzzy Systems." Computational and Mathematical Methods in Medicine 2012 (2012): 1–9. http://dx.doi.org/10.1155/2012/127130.
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Developing machine learning and soft computing techniques has provided many opportunities for researchers to establish new analytical methods in different areas of science. The objective of this study is to investigate the potential of two types of intelligent learning methods, artificial neural networks and neuro-fuzzy systems, in order to estimate breeding values (EBV) of Iranian dairy cattle. Initially, the breeding values of lactating Holstein cows for milk and fat yield were estimated using conventional best linear unbiased prediction (BLUP) with an animal model. Once that was established, a multilayer perceptron was used to build ANN to predict breeding values from the performance data of selection candidates. Subsequently, fuzzy logic was used to form an NFS, a hybrid intelligent system that was implemented via a local linear model tree algorithm. For milk yield the correlations between EBV and EBV predicted by the ANN and NFS were 0.92 and 0.93, respectively. Corresponding correlations for fat yield were 0.93 and 0.93, respectively. Correlations between multitrait predictions of EBVs for milk and fat yield when predicted simultaneously by ANN were 0.93 and 0.93, respectively, whereas corresponding correlations with reference EBV for multitrait NFS were 0.94 and 0.95, respectively, for milk and fat production.
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Andersen, S. "Calculation of response and variance reduction due to multi-stage and multiple trait selection." Animal Science 58, no. 1 (February 1994): 1–9. http://dx.doi.org/10.1017/s0003356100007017.
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AbstractIn deterministic comparisons of breeding schemes it is necessary to take account of variance reduction due to selection. This can take place as multi-stage selection within generations and it takes place across generations when offspring of selected parents are selected. A standard way to deal with this is to set up selection index equations where the parameters are altered as a consequence of selection. It is shown that if the breeding schemes use a univariate or multivariate best linear unbiased prediction (BLUP) animal model for prediction of breeding values this procedure can be simplified. This is done by modelling the distribution of estimated breeding value (EBV) utilizing that changes in EBV of an individual are independent of selection. In the univariate case the variance reduction and the resulting genetic gain can be calculated from the selection intensities and the accuracies in the unselected population. An expression is given for the response in each generation when selection is started in a base population with complete pedigree. This shows that a limiting value is obtained within three to four generations. The asymptotic response for several traits is described in the case where selection is on multitrait BLUP.
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Lee, Jungjae, SeokHyun Lee, Jong-Eun Park, Sung-Ho Moon, Sung-Woon Choi, Gwang-Woong Go, Dajeong Lim, and Jun-Mo Kim. "Genome-wide association study and genomic predictions for exterior traits in Yorkshire pigs1." Journal of Animal Science 97, no. 7 (May 14, 2019): 2793–802. http://dx.doi.org/10.1093/jas/skz158.
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Abstract The objectives of this study were to identify informative genomic regions that affect the exterior traits of purebred Korean Yorkshire pigs and to investigate and compare the accuracy of genomic prediction for response variables. Phenotypic data on body height (BH), body length (BL), and total teat number (TTN) from 2,432 Yorkshire pigs were used to obtain breeding values including as response variable the estimated breeding value (EBV) and 2 types of deregressed EBVs—one including the parent average (DEBVincPA) and the other excluding it (DEBVexcPA). A final genotype panel comprising 46,199 SNP markers was retained for analysis after quality control for common SNPs. The BayesB and BayesC methods—with various π and weighted response variables (EBV, DEBVincPA, or DEBVexcPA)—were used to estimate SNP effects, through the genome-wide association study. The significance of genomic windows (1 Mb) was obtained at 1.0% additive genetic variance and was subsequently used to identify informative genomic regions. Furthermore, SNPs with a high model frequency (≥0.90) were considered informative. The accuracy of genomic prediction was estimated using a 5-fold cross-validation with the K-means clustering method. Genomic accuracy was measured as the genomic correlation between the molecular breeding value and the individual weighted response variables (EBV, DEBVincPA, or DEBVexcPA). The number of identified informative windows (1 Mb) for BH, BL, and TTN was 4, 3, and 4, respectively. The number of significant SNPs for BH, BL, and TTN was 6, 4, and 5, respectively. Diversity π did not influence the accuracy of genomic prediction. The BayesB method showed slightly higher genomic accuracy for exterior traits than BayesC method in this study. In addition, the genomic accuracy using DEBVincPA as response variable was higher than that using other response variables. Therefore, the genomic accuracy using BayesB (π = 0.90) with DEBVinPA as a response variable was the most effective in this study. The genomic accuracy values for BH, BL, and TTN were calculated to be 0.52, 0.60, and 0.51, respectively.
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Greenwood, P. L., G. E. Gardner, and R. S. Hegarty. "Lamb myofibre characteristics are influenced by sire estimated breeding values and pastoral nutritional system." Australian Journal of Agricultural Research 57, no. 6 (2006): 627. http://dx.doi.org/10.1071/ar04318.
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The objective of this study was to establish the extent to which lamb myofibre characteristics at ~8 months of age were influenced by sire (n = 9) estimated breeding values (EBVs) and pasture-based nutritional systems (low and high quality and availability, LOW and HIGH) from birth to slaughter (n = 56). Immunostaining of myosin heavy chain isoforms in longissimus muscle fibres revealed that as the post-weaning eye muscle depth EBV (PEMD) increased, the percentage of type 2B/X myofibres increased and the percentage of type 2A myofibres decreased. The percentage of type 2B/X myofibres also increased with increasing PEMD in the semimembranosus muscle, but not in the semitendinosus muscle. Post-weaning fat depth (PFAT) EBV was negatively related with the percentage of type 2B/X myofibres in longissimus and semitendinosus muscles and with the relative area of more glycolytic to more oxidative fibre types, although there was an interaction with nutritional system in the semitendinosus muscle, with this ratio increasing with the PFAT EBV among the LOW nutrition lambs. Overall, post-weaning weight (PWWT) EBV had less effect on myofibre characteristics than PEMD and PFAT EBVs. Average cross-sectional area of myofibres was more affected by the LOW than HIGH nutritional system in longissimus muscle (–25%) compared with semitendinosus (–21%) and semimembranosus (–15%) muscles. LOW nutrition resulted in a significantly smaller cross-sectional area of all myofibre types in longissimus muscle and of types 2A, 2AB/X, and 2B/X in semimembranosus and semitendinosus muscles. Overall, the relative area of glycolytic myofibres increased and/or more oxidative myofibre types decreased in LOW compared with HIGH nutritional system lambs in longissimus and semimembranosus, but not in semitendinosus muscle. The results demonstrate significant influences of sire EBVs on myofibre characteristics of lambs, the extent of which depends upon muscle type and nutritional regimen. More specifically, they suggest continued selection for increased muscling and reduced fatness in lambs are associated with shifts in the proportions of myofibre types, with potential for adverse effects on eating quality. They also show that the direction and magnitude of the effects of chronic, moderate postnatal nutritional restriction at pasture on myofibre characteristics vary between muscles with different contractile, metabolic, and/or functional characteristics.
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Suryana, Muh M., B. J. Takaendengan, Umar Paputungan, and E. Pudjihastuti. "ESTIMASI NILAI PEMULIAAN DAN MPPA (Most Probable Producing Ability) KUDA PACU BERDASARKAN SIFAT KECEPATAN LARI." ZOOTEC 40, no. 2 (April 19, 2020): 392. http://dx.doi.org/10.35792/zot.40.2.2020.28295.
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ESTIMATION BREEDING VALUE AND MPPA (Most Probable Producing Ability) OF RACEHORSES BASED ON NATURE OF RUNNING SPEED. The aim of this study was to obtain the estimated number of breeding values from the racehorses parent in Minahasa for racehorse selection based on the superiority of genetic traits of speed. The descriptive analysis such asaverage, standard deviation and coefficient of variation of the speed and performance were done as the first step. Heritability, ripitability and the probability of breeding value (PBV) were calculated after all. The results of this study indicate that the value of heritability and repeatability obtained varies from low to high. The highest estimation of breeding value (PBV) for male (H), the highest MPPA (Most Probable Producing Ability) value in the population (individual B010) and the average MPPA value for the entire population were 0.0869, 0.1845 and 0.0239 respectively. The conclusion of this study puts the racehorse with the name "Swift Jhon" and "Super Princes" as males and individuals who have an average increase in the nature of the highest running speed. Keywords: Racehorse, Speed, EBV, MPPA
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Greenwood, P. L., G. E. Gardner, and R. S. Hegarty. "Indices of cellular development in muscles of lambs are influenced by sire estimated breeding values and pastoral nutritional system." Australian Journal of Agricultural Research 57, no. 6 (2006): 651. http://dx.doi.org/10.1071/ar05205.
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This study examined influences of sire (n = 9) estimated breeding values (EBVs), sire-group (Muscle, Growth, and Control), and nutrition (low and high quality and availability pasture) from birth to slaughter at ~8 months of age on indices of muscle cellularity and transcriptional and translational capacity in 56 castrate lambs. Effects of nutritional systems to 8 months of age were greater, overall, than those due to EBVs or sire-group. Amount of DNA increased with increasing EBV for post-weaning eye muscle depth (PEMD or Muscle EBV) in longissimus but not in semimembranosus and semitendinosus muscles, while Muscle EBV also had an inverse association with concentration of DNA. Protein to DNA and RNA to DNA were related positively to Muscle EBV, the associations being strongest for the semitendinosus muscle. Post-weaning weight (PWWT or Growth) EBV correlated positively with the RNA to DNA ratio and, among high but not low nutrition lambs, was inversely related to concentration of muscle DNA, whereas post-weaning fat depth (PFAT or Fat) EBV was correlated positively with RNA concentration. Overall, the magnitude of effects of sire-group was less than for sire EBVs, presumably due to differing selection pressures for muscling, fatness, and growth. High nutrition lambs had more protein to DNA than low nutrition lambs in the longissimus and semitendinosus muscles, but not in the semimembranosus muscle. In low compared with high nutrition lambs, concentration of DNA was greater in the longissimus and semitendinosus muscles. Total amount of DNA was reduced by more in low compared with high nutrition in the longissimus and semimembranosus than in the semitendinosus, and amount of protein was reduced by more in low compared with high nutrition in the longissimus than in the other two muscles. We conclude that genetic selection for eye muscle depth in sheep has differing effects on cellular characteristics of the longissimus, semimembranosus, and semitendinosus muscles, and has greater effects on muscle cellular characteristics than genetic selection for post-weaning weight or fat depth.
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Kennedy, B. W., V. M. Quinton, and C. Smith. "Genetic changes in Canadian performance-tested pigs for fat depth and growth rate." Canadian Journal of Animal Science 76, no. 1 (March 1, 1996): 41–48. http://dx.doi.org/10.4141/cjas96-006.
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Data on more than 1.3 million pigs of four breeds in four regions of Canada were used to estimate genetic changes in fat depth and growth rate from 1976 to 1993. Analysis was by a multi (two)-trait best linear unbiased prediction (BLUP) animal model within breed and across regions. The genetic changes were measured as the changes in average estimated breeding value (EBV) over years.The across-breed average total phenotypic changes from 1976 to 1993 were− 3.9 mm in fat depth (26% of the mean) and− 17 d in age at 100 kg (9% of the mean). The multi-trait BLUP estimates of the genetic trends were similar to single-trait BLUP estimates. The mean EBV and the changes were similar for the four regions. The changes were larger in the Landrace and Yorkshire breeds than in the Duroc and Hampshire. The overall genetic trends were − 1.44% of the mean yr−1 in fat depth and − 0.36% of the mean yr−1 in age at 100 kg. The trend for age at 100 kg increased over time as better methods of deriving the EBV were implemented. The current rates of pig improvement in Canada are good and yield large economic benefits. However, they could be improved to recoup the full gains possible through the Canadian Swine Improvement Program. Key words: Canadian pigs, performance testing, genetic trends
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Cheng, Jian, Rohan Fernando, and Jack C. Dekkers. "32 Cross validation of best linear unbiased predictions of breeding values using an efficient leave-one-out strategy." Journal of Animal Science 98, Supplement_4 (November 3, 2020): 10–11. http://dx.doi.org/10.1093/jas/skaa278.020.
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Abstract Efficient strategies have been developed for leave-one-out cross validation (LOOCV) of predicted phenotypes in a simple model with an overall mean and marker effects or animal genetic effects to evaluate the accuracy of genomic predictions. For such a model, the correlation between the predicted and the observed phenotype is identical to the correlation between the observed phenotype and the estimated breeding value (EBV). When the model is more complex, with multiple fixed and random effects, although the correlation between the observed and predicted phenotype can be obtained efficiently by LOOCV, it is not equal to the correlation between the observed phenotype and EBV, which is the statistic of interest. The objective here was to develop and evaluate an efficient LOOCV method for EBV or for predictions of other random effects under a general mixed linear model. The approach is based on treated all effects in the model, with large variances for fixed effects. Naïve LOOCV requires inverting the (n - 1) x (n - 1) dimensional phenotypic covariance matrix for each of the n (= no. observations) training data sets. Our method efficiently obtains these inverses from the inverse of the phenotypic covariance matrix for all n observations. Naïve LOOCV of EBV by pre-correction of fixed effects using the training data (Naïve LOOCV) and the new efficient LOOCV were compared. The new efficient LOOCV for EBV was 962 times faster than Naïve LOOCV. Prediction accuracies from the two strategies were the same (0.20). Funded by USDA-NIFA grant # 2017-67007-26144.
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Mielenz, N., and L. Schüler. "Konstruktion von Indizes mit Restriktionen in Random Regression Modellen zur Veränderung der Wachstumskurve." Archives Animal Breeding 50, no. 6 (October 10, 2007): 619–27. http://dx.doi.org/10.5194/aab-50-619-2007.
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Abstract. Title of the paper: Index construction with restrictions in random regression models to change the pattern of the growth curve Random regression models provide estimated breeding values (EBV) for the complete growth curve for any target age. The animal-specific curves can be described as the weighted sum of continuous covariates with random regression coefficients. By using the covariance matrix K of the additive genetic regression coefficients the response to index selection can be calculated for any age or time of the test period. In this study selection indexes with equality restrictions based on the eigenvectors of matrix K were used to modify the growth curve of the population. In order to demonstrate the index construction a matrix K was used, estimated from repeated measurements for body weight of bulls by using Legendre polynomials as covariates. Indexes for high and low growth rate until age at the reflection point were derived subject to the restriction of zero gain for initial and final body weight. Selection strategies for improving body weight at the end of the test period while holding the daily gain in a certain time interval on a desired level were compared. By using so-called "restrictive economic values", an aggregate breeding value for body weight was derived from EBV for individual growth curve.
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Ignat'eva, L., A. Konte, and A. Sermyagin. "To the question of evaluating the efficiency of linear breeding in Simmental cattle breed different origin." Agrarian Bulletin of the 197, no. 6 (June 20, 2020): 49–57. http://dx.doi.org/10.32417/1997-4868-2020-197-6-49-57.
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Abstract. The purpose of the research – to study the impact of related foreign pedigree resources on the Russian population of Simmental cattle. Research Methods. Studies carried out on cows of Simmental breed of different linear origin and genotypes in five regions of Russian Federation: Voronezh, Oryol, Kursk, Belgorod regions and Altayskiy krai, the total number was 35147 cows. EBV estimates were calculated through RENUMF 90, REMLF 90 and BLUPF 90 programs. Evaluation of the components of the variants of genetic and paratypical nature was carried out using the method restricted maximum likelihood – REML. Results. It is established that the largest share for animals foreign origin are 60.7 %, including German-Austrian bloodlines 46.6 % and Holsteins – 14.1 %. 39.3 % of animals are the Russian origin, which 13.5 % representatives of German-Austrian bloodlines, 17.8 % are Holsteins and 8.0 % are from domestic (Russian) bloodlines. In the general population of Simmental breed, the best productivity was shown by cows of German-Austrian bloodlines at the level of 5351 kg of milk with fat percentage 4.00 % and protein percentage 3.19 %. Representatives of German-Austrian bloodlines origin for milk yield showed the estimated breeding value (EBV) for Simmental bulls in the common population by +9.2 kg and fat percentage by +0.012 %. The negative EBV values were obtained for Russian bloodlines by –22.8 kg, and Holstein bloodlines took an intermediate position among all lines (+2.3 kg). The first calving cows, which were in the herd at the time of research, the best milk production traits were found in individuals of foreign origin, both for Holstein (6096 kg of milk with a fat content of 3.96 % and protein 3.23 %), and German-Austrian bloodlines (milk yield 5763 kg, fat 4.04 % and protein 3.19 %), with high estimates of breeding value for milk yield +33.3 kg and +15.2 kg, respectively. Low values of milk productivity among all evaluated animals were observed for animals of Russian bloodlines by 4469 kg milk 3.87 % fat and 3.20 % protein in milk. The first calving cows of Russian origin in foreign bloodlines origin exceeded their peers in Russian Simmental bloodlines in milk production by +608 kg of milk and +0.15 % fat (signed to German-Austrian bloodlines) and +924 kg and +0.06 % fat (signed to Holstein bloodlines). The average values of EBV in these lines, although had low values by –5.6 kg milk for Holstein and by +2.7 kg milk for German-Austrian bloodlines, but was significantly higher than for Russian lines by –12.7 kg milk. Scientific novelty. For the first time, scientific research aimed at improving the system of prediction to breeding abilities of bulls on dairy productivity of daughters based on optimization structure of equations of the mixed model (BLUP, the best linear unbiased prediction) has been carried out for the population Simmental cattle of Russian Federation.
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Huisman, A. E., D. J. Brown, and N. M. Fogarty. "Ability of sire breeding values to predict progeny bodyweight, fat and muscle using various transformations across environments in terminal sire sheep breeds." Animal Production Science 56, no. 1 (2016): 95. http://dx.doi.org/10.1071/an14666.
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Data used for the genetic evaluation of the terminal sire sheep breeds in Australia originate from a large range of genotypes and environments. This means there are large differences in the level of production and therefore contemporary group means and variances within the data. This study examined four transformations to account for the heterogeneity of variance in the observed data and their effect on the ability of estimated breeding values of sires (sire EBV) to predict progeny performance. This predictive ability was described by regressing offspring performance on sire EBV. The expected value of this regression is 0.5, which indicates that half of the sire EBV differences can be expected in the progeny. The transformations of observed data were investigated in low, medium and high production environments for weight and ultrasound scan traits (fat and muscle) in terminal sire sheep breeds. There were records from over 300 000 sheep in the LAMBPLAN terminal sire dataset, predominately from Poll Dorset, Texel, Suffolk and White Suffolk breeds. The transformation methods applied to the observed data were: traits expressed as a percentage of the contemporary group mean; traits re-scaled to a common contemporary group mean in units of measurement; a logarithmic transformation; and a square root transformation. The heritabilities and other variance ratios estimated from the transformed traits were not significantly different from those using the observed data. Phenotypes transformed to a proportion of the contemporary group mean, either as a percentage or in units of measurement, resulted in the most consistent EBV across all production environments for weight and fat traits, with little effect of transformations for muscle traits. The transformation of data to the contemporary mean in units of measurement for weight and fat traits has been implemented in the Sheep Genetics evaluation system. The consistency of the progeny–sire EBV regressions around 0.5 in the data from these purebred industry flocks is heartening for terminal sire evaluation.
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Magnabosco, Cláudio U., Fernando Lopes, Valentina Magnabosco, Raysildo Lobo, Leticia Pereira, Rafael Espigolan, and Ludmilla Brunes. "PSXII-22 Genomic prediction accuracy for feed efficiency related traits using different pseudo-phenotypes, prediction and validation methods in Nellore cattle." Journal of Animal Science 98, Supplement_4 (November 3, 2020): 245–46. http://dx.doi.org/10.1093/jas/skaa278.446.
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Abstract The aim of the study was to evaluate prediction methods, validation approaches and pseudo-phenotypes for the prediction of the genomic breeding values of feed efficiency related traits in Nellore cattle. It used the phenotypic and genotypic information of 4,329 and 3,594 animals, respectively, which were tested for residual feed intake (RFI), dry matter intake (DMI), feed efficiency (FE), feed conversion ratio (FCR), residual body weight gain (RG), and residual intake and body weight gain (RIG). Six prediction methods were used: ssGBLUP, BayesA, BayesB, BayesCπ, BLASSO, and BayesR. Three validation approaches were used: 1) random: where the data was randomly divided into ten subsets and the validation was done in each subset at a time; 2) age: the division into the training (2010 to 2016) and validation population (2017) were based on the year of birth; 3) genetic breeding value (EBV) accuracy: the data was split in the training population being animals with accuracy above 0.45; and validation population those below 0.45. We checked the accuracy and bias of genomic value (GEBV). The results showed that the GEBV accuracy was the highest when the prediction is obtained with ssGBLUP (0.05 to 0.31) (Figure 1). The low heritability obtained, mainly for FE (0.07 ± 0.03) and FCR (0.09 ± 0.03), limited the GEBVs accuracy, which ranged from low to moderate. The regression coefficient estimates were close to 1, and similar between the prediction methods, validation approaches, and pseudo-phenotypes. The cross-validation presented the most accurate predictions ranging from 0.07 to 0.037. The prediction accuracy was higher for phenotype adjusted for fixed effects than for EBV and EBV deregressed (30.0 and 34.3%, respectively). Genomic prediction can provide a reliable estimate of genomic breeding values for RFI, DMI, RG and RGI, as to even say that those traits may have higher genetic gain than FE and FCR.
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Rajkumar, U., L. Leslie Leo Prince, K. S. Rajaravindra, S. Haunshi, M. Niranjan, and R. N. Chatterjee. "Analysis of (co) variance components and estimation of breeding value of growth and production traits in Dahlem Red chicken using pedigree relationship in an animal model." PLOS ONE 16, no. 3 (March 3, 2021): e0247779. http://dx.doi.org/10.1371/journal.pone.0247779.
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Variance and covariance components of growth and production traits were analyzed employing REML animal model to assess the Dahlem Red (PD-3) chicken population for direct additive genetic, maternal effects and to estimate the estimated breeding value (EBV), genetic parameters, genetic trends and rate of inbreeding (ΔF) utilizing seven generation’s data. The generation and hatch had significant (P≤0.01) effect on the body weight at 0 day (BW0), 2 (BW2), 4 (BW4) and 6 weeks (BW6) and shank length at six weeks of age (SL6). The average least squares means (LSM) for BW6 and SL6 were 273.93±0.62 g and 53.97±0.05 mm, respectively. All the production traits were significantly (P≤0.01) influenced by generation and hatch. The average LSM for age at sexual maturity (ASM), egg production up to 40 weeks (EP40) and egg mass up to 40 weeks (EM40) were 168.82±0.25 d, 72.60±0.41 eggs and 4.21±0.07 kg, respectively. Model 5 with additive direct, maternal genetic, maternal permanent environmental and residual variance components was the best for BW0, BW2 and BW4 based on the AIC values obtained in WOMBAT. Model 4 was the best model for BW6, SL6, ASM, EP40 and EM40 with additive direct, maternal permanent environmental and residual variance components. Maternal effects were higher during early age, decreased with age, and remained present until 20 weeks of age. The heritability (h2) estimates were low to moderate in magnitude for all the growth traits and ranged from 0.02±0.03 to 0.19±0.03. The maternal heritability was high at hatch (0.35±0.06), decreased gradually until 4th week (0.02±0.01) and ceased afterwards. The heritabilities of EP40 (0.11±0.03) and EM40 (0.12±0.04) were low. The direct additive genetic correlations (ra) between BW2, BW4, BW6 and SL6 were high and positive (P≤ 0.05). The additive genetic and maternal permanent environmental correlation between EP40 and EM40 were high and positive (P≤ 0.05). The EBV of EM40 was significant (P≤ 0.05) with 0.48 kg/generation in PD-3 chicken at the end of the seventh generation. The EBV of EP40 showed an increasing trend with a genetic gain of 1.87 eggs per generation. The average inbreeding coefficient of the population was 0.019 and average ΔF was 0.007 over the last seven generations of selection. The EBV trends for primary and associated traits showed linear trends in the desired direction and negligible inbreeding.
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Ali, A., K. Javed, I. Zahoor, and K. M. Anjum. "Analysis of non-genetic and genetic influences underlying the growth of Kajli lambs." South African Journal of Animal Science 50, no. 4 (October 29, 2020): 613–25. http://dx.doi.org/10.4314/sajas.v50i4.13.
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Data on 2931 Kajli lambs, born from 2007 to 2018, were used to quantify environmental and genetic effects on growth performance of Kajli sheep. Traits considered for evaluation were birth weight (BWT), 120-day adjusted weight (120DWT), 180-day adjusted weight (180DWT), 270-day adjusted weight (270DWT), and 365-day adjusted weight (365DWT). Fixed effects of year of birth, season of birth, sex, birth type, and dam age on these traits were evaluated using linear procedures of SAS, 9.1. Similarly, BWT, 120DWT, 180DWT, and 270DWT were used as fixed effects mixed model analyses. Variance components, heritability and breeding values were estimated by restricted maximum likelihood. The genetic trend for each trait was obtained by regression of the estimated breeding values (EBV) on year of birth. Analyses revealed substantial influence of birth year on all traits. Sex and birth type were the significant sources of variation for BWT and 120DWT. Season of birth did not influence birth weight meaningfully, but had a significant role in the expression of 120DWT, 180DWT, and 270DWT. Heritability estimates were generally low (0.003 ± 0.018 to 0.099 ± 0.067) for all traits. With the exception of the genetic correlation of 180DWT and 365DWT, the genetic correlations between trait were strong and positive. Only 365DWT had a positive genetic trend. Although the heritability estimates for almost all weight traits were low, high and positive genetic correlations between BWT and other weight traits suggest that selection based on BWT would result in the improvement of other weight traits as a correlated response.Keywords: bodyweight, breeding value, genetic correlation, sheep
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Stephens, M. Joseph, Jessica Scalzo, Peter A. Alspach, Ron A. Beatson, and Ann Marie Connor. "Genetic Variation and Covariation of Yield and Phytochemical Traits in a Red Raspberry Factorial Study." Journal of the American Society for Horticultural Science 134, no. 4 (July 2009): 445–52. http://dx.doi.org/10.21273/jashs.134.4.445.
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Breeding for high yield is a major objective of most small fruit breeding programs worldwide. In recent years, research associated with health benefits of berry fruit has resulted in some breeding programs looking for material with improved health properties with the goal of incorporating these into genotypes with high yield and other favorable agronomic characters. In this study, we estimated variance components, heritabilities, and phenotypic and genotypic correlations for yield components and phytochemicals [total phenolics (TPH), antioxidant activity (FRAP), and total anthocyanins (TACY)] from 828 genotypes in a red raspberry (Rubus idaeus) factorial mating design based on 42 full-sib families derived from seven female and six male parents harvested in one season in New Zealand. Narrow sense heritability estimates varied from moderately low [0.23 for percent budburst (PCBB)] to high [0.82 for mean berry weight (BWT)]. Highest genotypic correlations with total yield (TYLD) were found for mean cane length (0.60) followed by moderate correlations for PCBB (0.38), BWT (0.34) and fruit number per unit lateral (0.31). For these four components, the correlation between the product of the empirical breeding values (eBV) and TYLD was as good (0.67) as the correlation between the product of the seven yield components measured (0.68). Moderately high negative genotypic correlations were found between TYLD and TPH (–0.67), FRAP (–0.68), and TACY (–0.64), suggesting that breeding for high-yielding genotypes may result in reduced phytochemical levels. A pigment-deficient R. parvifolius × R. idaeus hybrid derivative parent (R. parv deriv) had the most influence on berry weight as a yield component. Removal of the R. parv deriv progeny from the analysis increased the contribution of berry weight to total yield. Heritability estimates were generally lower when the R. parv deriv crosses were omitted, particularly for number of canes BWT, TYLD, and the phytochemicals. Implications of R. parv deriv crosses on these results are discussed. Of the 828 genotypes, only five had an eBV for total yield greater than that of the best yielding parent, whereas 49 had larger berries than the best parent. None of the 828 genotypes had an eBV for yield components or phytochemicals less than that of the lowest parent, whereas 13 had a higher eBV associated with phytochemicals than that of the highest parent.
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Baller, Johnna L., Stephen D. Kachman, Larry A. Kuehn, and Matthew L. Spangler. "38 Using pooled data for single-step genomic prediction: Impact of within-pool variance and size." Journal of Animal Science 98, Supplement_4 (November 3, 2020): 9. http://dx.doi.org/10.1093/jas/skaa278.017.
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Abstract Economically relevant traits (ERT) are routinely collected within commercial segments of the beef industry but are rarely included in genetic evaluations because of unknown pedigrees. Individual relationships could be resurrected with genomics, which would be costly; pooling DNA and phenotypic data provides a cost-effective solution. A simulated beef cattle population consisting of 15 generations was genotyped with approximately 50k markers (841 quantitative trait loci were located across the genome) and phenotyped for a moderately heritable trait. Individuals from generation 15 were included in pools (observed genotype and phenotype were mean values of a group). Estimated breeding values (EBV) were generated from a single-step GBLUP model. The effects of pooling strategy (random and minimizing or uniformly maximizing phenotypic variation), pool size (1, 2, 10, 20, 50, 100, or no data from generation 15), and generational gaps of genotyping on EBV accuracy (correlation of EBV with true breeding values) were quantified. Greatest EBV accuracies of sires and dams were observed when no gap between genotyped parents and pooled offspring occurred. The EBV accuracies resulting from pools were greater than no data from generation 15 regardless of sire or dam genotyping. Minimizing phenotypic variation increased EBV accuracy by 8% and 9% over random pooling and uniformly maximizing phenotypic variation, respectively. Pool size of 2 was the only scenario that did not significantly decrease EBV accuracy compared to individual data when pools were formed randomly or by uniformly maximizing phenotypic variation (P > 0.05). Pool sizes of 2, 10, 20, or 50 did not generally lead to EBV accuracies that were statistically different than individual data when pools were constructed to minimize phenotypic variation (P > 0.05). Pooled genotyping to garner commercial-level phenotypes for genetic evaluations seems plausible, although differences exist depending on pool size and pool formation strategy. The USDA is an equal opportunity employer.
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Fu, Donghai, Xiaoming Ma, Congjun Jia, Min Chu, Qinhui Lei, Zhiping Wen, Xiaoyun Wu, et al. "A Study of Genomic Prediction of 12 Important Traits in the Domesticated Yak (Bos grunniens)." Animals 9, no. 11 (November 7, 2019): 927. http://dx.doi.org/10.3390/ani9110927.
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The aim of this study was to explore the possibility of applying GP to important economic traits in the domesticated yak, thus providing theoretical support for its molecular breeding. A reference population was constructed consisting of 354 polled yaks, measuring four growth traits and eight hematological traits related to resistance to disease (involved in immune response and phagocytosis). The Illumina bovine HD 770k chip was used to obtain SNP information of all the individuals. With these genotypes and phenotypes, GBLUP, Bayes B and Bayes Cπ methods were used to predict genomic estimated breeding values (GEBV) and assess prediction capability. The correlation coefficient of the association of GEBV with estimated breeding value (EBV) was used as PA for each trait. The prediction accuracy varied from 0.043 to 0.281 for different traits. Each trait displayed similar PAs when using the three methods. Lymphocyte counts (LYM) exhibited the highest predictive accuracy (0.319) during all GP, while chest girth (CG) provided the lowest predictive accuracy (0.043). Our results showed moderate PA in most traits such as body length (0.212) and hematocrit (0.23). Those traits with lower PA could be improved by using SNP chips designed specifically for yak, a better optimized reference group structure, and more efficient statistical algorithms and tools.
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Lewis, R. M., R. E. Crump, G. Simm, and R. Thompson. "Assessing connectedness in across-flock genetic evaluations." Proceedings of the British Society of Animal Science 1999 (1999): 121. http://dx.doi.org/10.1017/s1752756200002763.
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With across-flock genetic evaluations, the extent of genetic links or connectedness between animals in separate flocks affects the reliability of selection decisions. As connectedness improves, error in comparing breeding values among flocks falls. Connectedness is thought more important when founder animals (i.e. unknown parentage) of separate flocks differ genetically. The prediction error variance (PEV) of differences in estimated breeding values (EBV) between animals is considered an appropriate measure of connectedness (Kennedy and Trus, 1993). In this study the level of connectedness, and its consequence, in breeding schemes that differ in the extent of ancestral relationships between flocks, and in which founder animals of these flocks differ genetically, was assessed by stochastic simulation.
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Velazco, J. I., R. M. Herd, D. J. Cottle, and R. S. Hegarty. "Daily methane emissions and emission intensity of grazing beef cattle genetically divergent for residual feed intake." Animal Production Science 57, no. 4 (2017): 627. http://dx.doi.org/10.1071/an15111.
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As daily methane production (DMP; g CH4/day) is strongly correlated with dry matter intake (DMI), the breeding of cattle that require less feed to achieve a desired rate of average daily gain (ADG) by selection for a low residual feed intake (RFI) can be expected to reduce DMP and also emission intensity (EI; g CH4/kg ADG). An experiment was conducted to compare DMP and EI of Angus cattle genetically divergent for RFI and 400-day weight (400dWT). In a 6-week grazing study, 64 yearling-age cattle (30 steers, 34 heifers) were grazed on temperate pastures, with heifers and steers grazing separate paddocks. Liveweight (LW) was monitored weekly and DMP of individual cattle was measured by a GreenFeed emission monitoring unit in each paddock. Thirty-nine of the possible 64 animals had emission data recorded for 15 or more days, and only data for these animals were analysed. For these cattle, regression against their mid-parent estimated breeding value (EBV) for post-weaning RFI (RFI-EBV) showed that a lower RFI-EBV was associated with higher LW at the start of experiment. Predicted dry matter intake (pDMI), predicted DMP (pDMP) and measured DMP (mDMP) were all negatively correlated with RFI-EBV (P < 0.05), whereas ADG, EI, predicted CH4 yield (pMY; g CH4/kg DMI) were not correlated with RFI-EBV (P > 0.1). Daily CH4 production was positively correlated with animal LW and ADG (P < 0.05). The associations between ADG and its dependent traits EI and pMY and predicted feed conversion ratio (kg pDMI/kg ADG) were strongly negative (r = –0.82, –0.57 and –0.85, P < 0.001) implying that faster daily growth by cattle was accompanied by lower EI, MY and feed conversion ratio. These results show that cattle genetically divergent for RFI do not necessarily differ in ADG, EI or pMY on pasture and that, if heavier, cattle with lower RFI-EBV can actually have higher DMP while grazing moderate quality pastures.
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Hall, D. G., A. R. Gilmour, N. M. Fogarty, and P. J. Holst. "Growth and carcass composition of second-cross lambs. 2. Relationship between estimated breeding values of sires and their progeny performance under fast and slow growth regimes." Australian Journal of Agricultural Research 53, no. 12 (2002): 1341. http://dx.doi.org/10.1071/ar01194.
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Growth and carcass performance of 2316 ewe and cryptorchid second-cross lambs over 2 years was related to the LAMBPLAN estimated breeding values (EBVs) of their sires. The lambs (56–156 per sire) were sired by 20 Poll Dorset rams from one stud, which were selected to represent a range of EBVs for growth rate and leanness. Half of each lamb sex group was grown at a fast rate from weaning to slaughter at 40 kg liveweight for ewes or 48 kg for cryptorchids. The other half was grown at a slower rate to the same slaughter weights, 10–13 weeks later. Lamb measurements included liveweight approximately every 21 days to slaughter, and fat and muscle depth on live lambs using ultrasound and carcass fat depth. The regressions of lamb weight on sire EBV for weight increased as the lambs aged and were 0.243 ± 0.124 for fasted weight pre-slaughter and 0.158 ± 0.064 for carcass weight. Live lamb C fat depth (45 mm from the mid-line over the 12th rib), carcass C fat depth, and carcass GR (total tissue depth 110 mm from the mid-line of the carcass over the 12th rib) were all related to sire EBV for fat. The regression values for ultrasound C fat depth and carcass GR of 0.156 ± 0.049 and 0.366 ± 0.159 on the sire EBV for fat (mm/mm EBV) were higher than the expected values. The results demonstrate that over a range of sires, 2 years, 2 sexes, and different nutrition regimes there are significant advantages in progeny weight and leanness if sires are selected for high EBVs for weight and leanness.
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Weaver, Andrew R., Donald L. Wright, Scott P. Greiner, and Scott A. Bowdridge. "197 Utilization of Katahdin rams with lower fecal egg count estimated breeding values improves parasite resistance and fitness traits of progeny." Journal of Animal Science 97, Supplement_1 (July 2019): 78. http://dx.doi.org/10.1093/jas/skz053.178.
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Abstract Genetic selection for internal parasite resistance in sheep is a valuable tool to mitigate effects of parasitism especially when significant within breed variability exists. To better understand the mechanism underpinning this variability, a divergent mating scheme was established. Katahdin rams (n = 4) were selected based on their estimated breeding value (EBV) for fecal egg count (FEC) and grouped as numerically high (HiFEC; n = 2) or low (LoFEC; n = 2). Rams were randomly mated to Katahdin ewes at the Southwest Virginia Agriculture Research and Extension Center. Lambs were born mid-March and managed as one group, then weaned in mid-June. Lambs were transported to the WVU Animal Sciences Farm where they were randomly allocated to four pens with even distribution of sire and sex. All lambs (n = 109) were infected with 10,000 H. contortus L3 and the infection persisted for 5 weeks. Weights, FEC, and packed cell volume (PCV) were collected weekly. Statistical analysis was performed using the Mixed Model procedure and repeated measures in SAS with fixed effects of sire group. Weaning FEC was numerically greater for HiFEC-sired lambs vs. LoFEC-sired lambs (2914 vs. 1821 eggs/g; respectively). However, death loss for HiFEC-sired lambs tended to be almost twice that of LoFEC-sired lambs (20% vs. 11%, P = 0.09; respectively). Weaning weights did not differ. Fecal egg count from the prepatent to patent period was greater in HiFEC vs. LoFEC-sired lambs (210 vs. 34 eggs/g; P = 0.05). Packed cell volume was numerically lower in HiFEC-sired lambs. There were no differences in post-weaning growth, ultrasound fat thickness, or loin depth in lambs from divergent sire groups. These data indicate that utilizing LoFEC EBV sires reduces FEC and improves disease resistance in progeny without affecting growth or carcass traits
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Grundy, B., and WG Hill. "A method for reducing inbreeding with Best Linear Unbiased Prediction." Proceedings of the British Society of Animal Production (1972) 1993 (March 1993): 33. http://dx.doi.org/10.1017/s030822960002362x.
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An optimum way of selecting animals is through a prediction of their genetic merit (estimated breeding value, EBV), which can be achieved using a best linear unbiased predictor (BLUP) (Henderson, 1975). Selection decisions in a commercial environment, however, are rarely made solely on genetic merit but also on additional factors, an important example of which is to limit the accumulation of inbreeding. Comparison of rates of inbreeding under BLUP for a range of hentabilities highlights a trend of increasing inbreeding with decreasing heritability. It is therefore proposed that selection using a heritability which is artificially raised would yield lower rates of inbreeding than would otherwise be the case.
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Hradecká, E., J. Čítek, L. Panicke, V. Řehout, and L. Hanusová. "The relation of GH1, GHR and DGAT1 polymorphisms with estimated breeding values for milk production traits of German Holstein sires." Czech Journal of Animal Science 53, No. 6 (June 19, 2008): 238–46. http://dx.doi.org/10.17221/362-cjas.
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: We analysed the relations of estimated breeding values (EBV) of 315 German Holstein sires to their genotypes in growth hormone gene (<i>GH1</i>), growth hormone receptor gene (<i>GHR</i>) and acylCoA-diacylglycerol acyltransferase 1 (<i>DGAT1</i>). The strong relation of <i>DGAT1 K232A</i> to the estimated breeding values for milk production traits has been confirmed, when allele <i>DGAT1<sup>K</sup></i> was connected with higher milk fat yield, milk fat and milk protein content, while allele <i>DGAT1<sup>A</sup></i> increased milk yield and milk protein yield. The effect of <i>DGAT1</i> genotype explained from 4.70% of variability of EBVs for fat yield to 31.90% of variability of EBVs for fat content. The evaluation of <i>GH1</i> 127 Leu/Val and <i>GHR</i> 257 SNP polymorphisms did not reveal an association of their polymorphism with EBVs for milk production traits, except the EBVs of <i>GHR<sup>G</sup>/GHR<sup>G</sup></i> homozygotes for fat yield, which were significantly lower. The effect of <i>GH1</i> or <i>GHR genotype explained only a negligible portion of variability of EBVs (<i>R</i><sup>2</sup> < 1.00% in most cases).
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Burke, J. M., D. R. Notter, and J. E. Miller. "105 Sire's Estimated Breeding Value (EBV) for Fecal Egg Count (FEC) Influences BW, FEC, and Anemia Measures of Offspring in Katahdin Sheep." Journal of Animal Science 95, suppl_1 (December 1, 2016): 52. http://dx.doi.org/10.2527/ssasas2017.0105.
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Hopkins, D. L., R. S. Hegarty, and T. C. Farrell. "Relationship between sire estimated breeding values and the meat and eating quality of meat from their progeny grown on two planes of nutrition." Australian Journal of Experimental Agriculture 45, no. 5 (2005): 525. http://dx.doi.org/10.1071/ea03175.
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The meat of 140 female lambs was examined. These lambs were sired by 9 Poll Dorset sires (3 selected for growth, 3 for muscling and 3 control) and fed either a low or high plane of nutrition from birth to slaughter. All carcasses were electrically stimulated and portions of M. longissimus thoracis et lumborum (loin) aged for 5 days before freezing. Subsequently, 10 consumers tested each portion for eating quality traits. A portion of the same muscle from the opposing side of the carcass was divided into 3 sections and aged for either 1, 3 or 5 days and then used to measure shear force (objective tenderness). Portions of the M. semimembranosus (topside) were also aged for 3 or 5 days and subjected to shear testing. Low plane animals produced tougher loins (based on shear force). As ultimate pH increased, shear force of the loin increased for low plane animals, while for high plane animals there was no such effect. This latter group had significantly lower ultimate pH values in all 3 muscles tested. Plane of nutrition had the greatest effect on topside shear force with low plane lambs producing tougher topsides. As ultimate pH increased, the topsides became tougher and as expected ageing improved the tenderness. There was no effect of sire EBVs (estimated breeding values) on shear force or objective meat quality traits apart from loin lightness which increased as the EBV for post-weaning weight (PWWT) increased and intramuscular fat in the loin which decreased as sire EBV for post-weaning muscle depth (PEMD) increased. Plane of nutrition did not have a significant effect on eating quality attributes as assessed by consumers. There was, however, an effect of sire EBV for muscling (PEMD) on tenderness, juiciness, flavour and overall liking, such that increased EBV led to decreased scores for the sensory traits. The findings suggest selection of sires for increasing PEMD will have a detrimental affect on the eating quality of their progeny, but this will not be reflected in shear force values or other objective meat quality traits apart from intramuscular fat. The effects of a low plane of nutrition on eating quality were minimal and largely controlled by the use of best practice processing, but were evident for a number of meat quality traits.
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Nwogwugwu, Chiemela Peter, Yeongkuk Kim, Hyunji Choi, Jun Heon Lee, and Seung-Hwan Lee. "Assessment of genomic prediction accuracy using different selection and evaluation approaches in a simulated Korean beef cattle population." Asian-Australasian Journal of Animal Sciences 33, no. 12 (December 1, 2020): 1912–21. http://dx.doi.org/10.5713/ajas.20.0217.
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Objective: This study assessed genomic prediction accuracies based on different selection methods, evaluation procedures, training population (TP) sizes, heritability (h<sup>2</sup>) levels, marker densities and pedigree error (PE) rates in a simulated Korean beef cattle population.Methods: A simulation was performed using two different selection methods, phenotypic and estimated breeding value (EBV), with an h<sup>2</sup> of 0.1, 0.3, or 0.5 and marker densities of 10, 50, or 777K. A total of 275 males and 2,475 females were randomly selected from the last generation to simulate ten recent generations. The simulation of the PE dataset was modified using only the EBV method of selection with a marker density of 50K and a heritability of 0.3. The proportions of errors substituted were 10%, 20%, 30%, and 40%, respectively. Genetic evaluations were performed using genomic best linear unbiased prediction (GBLUP) and single-step GBLUP (ssGBLUP) with different weighted values. The accuracies of the predictions were determined.Results: Compared with phenotypic selection, the results revealed that the prediction accuracies obtained using GBLUP and ssGBLUP increased across heritability levels and TP sizes during EBV selection. However, an increase in the marker density did not yield higher accuracy in either method except when the h<sup>2</sup> was 0.3 under the EBV selection method. Based on EBV selection with a heritability of 0.1 and a marker density of 10K, GBLUP and ssGBLUP_0.95 prediction accuracy was higher than that obtained by phenotypic selection. The prediction accuracies from ssGBLUP_0.95 outperformed those from the GBLUP method across all scenarios. When errors were introduced into the pedigree dataset, the prediction accuracies were only minimally influenced across all scenarios.Conclusion: Our study suggests that the use of ssGBLUP_0.95, EBV selection, and low marker density could help improve genetic gains in beef cattle.
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McHugh, N., T. Pabiou, K. McDermott, E. Wall, and D. P. Berry. "Impact of birth and rearing type, as well as inaccuracy of recording, on pre-weaning lamb phenotypic and genetic merit for live weight1." Translational Animal Science 1, no. 2 (April 1, 2017): 137–45. http://dx.doi.org/10.2527/tas2017.0015.
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Abstract The objective of the present study was to quantify the impact of the systematic environmental effects of both birth and rearing type on pre-weaning lamb live weight, and to evaluate the repercussions of inaccurate recording of birth and rearing type on subsequent genetic evaluations. A total of 32,548 birth weight records, 35,770 forty-day weight records and 32,548 records for average daily gain (ADG) between birth and 40-day weight from the Irish national sheep database were used. For each lamb, a new variable, birth-rearing type, reflecting both the birth and rearing type of a lamb was generated by concatenating both parameters. The association between birth-rearing type and birth weight, 40-day weight, and ADG was estimated using linear mixed models. The repercussions of inaccurate recording of birth type were determined by quantifying the impact on sire estimated breeding value (EBV; with an accuracy of ≥ 35%), where one of the lambs born in a selection of twin litter births was assumed to have died at birth but the farmer recorded the birth and rearing type as a singleton. The heaviest mean birth weight was associated with lambs born and subsequently reared as singles (5.47 kg); the lightest mean birth weight was associated with lambs born and reared as triplets (4.10 kg). The association between birth-rearing type and 40-day weight differed by dam parity (P < 0.001). Lambs reared by first parity dams as singles, irrespective of birth type were, on average, heavier at 40-day weighing than lambs reared as multiples, but as parity number increased, single-born lambs reared as twins outperformed triplet-born lambs reared as singles. Irrespective of the trait evaluated, the correlation between sire EBV estimated from the accurately recorded data and sire EBV estimated from the data with recording errors was strong ranging from 0.93 (birth weight) to 0.97 (ADG). The EBV for sires with progeny data manipulated were 0.14 kg, 0.34 kg and 5.56 g/d less for birth weight, 40-day weight and ADG, respectively, compared to their equivalent EBV calculated using accurately recorded data. Results from this study highlight the importance of precise recording of birth-rearing type by producers for the generation of accurate genetic evaluations.
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Pawlik, Adrianna, Grażyna Sender, Magdalena Sobczyńska, Agnieszka Korwin-Kossakowska, Henryka Lassa, and Jolanta Oprządek. "Lactoferrin gene variants, their expression in the udder and mastitis susceptibility in dairy cattle." Animal Production Science 55, no. 8 (2015): 999. http://dx.doi.org/10.1071/an13389.
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Lactoferrin gene (LF) is regarded as one of the potential markers of mastitis susceptibility/resistance in dairy cattle. The study’s aim was therefore, to investigate the feasibility of two single nucleotide polymorphisms (SNP), placed in the 5′-flanking region and 3′-untranslated region of the LF gene, to serve as mastitis markers. The associations between these SNP and the expression of LF, both on mRNA and protein level, were estimated in the milk of Polish Holstein-Friesian cows. The relationships between polymorphisms and cows’ estimated breeding values (EBV) for somatic cell count were also calculated. It was shown that both polymorphisms have a significant impact on lactoferrin content in milk, and that LF+32 SNP is associated with the cow’s EBV for somatic cell count. No association between SNP chosen for the study and lactoferrin mRNA abundance in milk somatic cells was observed. We propose LF+32 SNP for a molecular marker of mastitis resistance in dairy cows.
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Lourenco, Daniela, Shogo Tsuruta, Yutaka Masuda, and Ignacy Misztal. "384 Genetic and Genomic Analysis in Livestock with Increasing Datasets." Journal of Animal Science 98, Supplement_4 (November 3, 2020): 137–38. http://dx.doi.org/10.1093/jas/skaa278.253.
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Abstract In animal breeding and genetics, statistical methods have been used for several decades to identify animals with the best genetic potential. One of the foundations for computing accurate estimated breeding values (EBV) is the amount of data that is used in the evaluation system — as the more data points one animal has, the more accurate its EBV is going to be. However, the animal breeding and genetics field periodically faces a big data paradox, where efficient methods have to be developed to handle the amount of data collected over time, given the computing capacity becomes the limiting factor. For instance, running genetic evaluations based on phenotypes and pedigree for a million animals was impossible in 1970. Methods and algorithms evolved to a point where using data for millions of animals was not a problem, until genomic information became available. After the development of single nucleotide polymorphism (SNP) chips for livestock in 2008, genomic information started being used in addition to phenotypes and pedigree to further improve accuracy of EBV. However, each animal is genotyped for around 50,000 SNP, which makes this data dense and difficult to work with. Over 790,000 Angus and 3.4 million Holstein cattle have been genotyped in the US as of April 2020. As the amount of new data considerably increases every week, most of the genomic evaluations are done on a weekly basis. Given that data have to be processed, the computation of EBV cannot take more than four days, which can be challenging depending on the model. In this talk we will discuss the challenges and solutions for successful genomic evaluations in large livestock populations. Finally, perspectives on the use of whole-genome sequence data and high-throughput phenotypes in genomic analysis will be summarized.
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Lidauer, Martin, and Esa Mäntysaari. "Detection of bias in animal model pedigree indices of heifers." Agricultural and Food Science 5, no. 4 (July 1, 1996): 387–97. http://dx.doi.org/10.23986/afsci.72751.
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The objective of the study was to test whether the pedigree indices (PI) of heifers are biased, and if so, whether the magnitude of the bias varies in different groups of heifers. Therefore, two animal model evaluations with two different data sets were computed. Data with all the records from the national evaluation in December 1994 was used to obtain estimated breeding values (EBV) for 305-days’ milk yield and protein yield. In the second evaluation, the PIs were estimated for cows calving the first time in 1993 by excluding all their production records from the data. Three different statistics, a simple t-test, the linear regression of EBV on PI, and the polynomial regression of the difference in the predictions (EBV-PI) on PI, were computed for three groups of first parity Ayrshire cows: daughters of proven sires, daughters of young sires, and daughters of bull dam candidates. A practically relevant bias was found only in the PIs for the daughters of young sires. On average their PIs were biased upwards by 0.20 standard deviations (78.8 kg) for the milk yield and by 0.21 standard deviations (2.2 kg) for the protein yield. The polynomial regression analysis showed that the magnitude of the bias in the PIs changed somewhat with the size of the PIs.
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Weisz, F., T. Urban, P. Chalupová, and A. Knoll. "Association analysis of seven candidate genes with performance traits in Czech Large White pigs." Czech Journal of Animal Science 56, No. 8 (August 18, 2011): 337–44. http://dx.doi.org/10.17221/169/2010-cjas.
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In this study association analyses were performed between genes tagged SNP (IGF2, NAMPT, DGAT1, MYF4, MC3R, MC4R and MYOD1), performance traits (backfat thickness, lean meat content, average daily gain from birth to the end of the test, average daily gain in test) and estimated breeding values (EBVs) in a population of Czech Large White sows (n = 101). Genotyping of all SNPs was performed by SNapShot with the exception of SNP within NAMPT gene for which HpaII PCR-RFLP assay was used. The following significant associations between genes tagged SNPs and traits or EBVs were found out: DGAT1 – lean meat content (AG > AA, P ≤ 0.05), MC4R – EBV for lean meat content (GG > AA, P ≤ 0.05; GG > AG, P ≤ 0.05), IGF2 – EBV for reproduction (piglets born alive in the second and subsequent parity) (AG > AA, P ≤ 0.05) and total EBV (AG > AA, P ≤ 0.01) and MC3R – EBV for average daily gain (CT > TT, P ≤ 0.05).
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Buzanskas, M. E., R. P. Savegnago, D. A. Grossi, G. C. Venturini, S. A. Queiroz, L. O. C. Silva, R. A. A. Torres Júnior, D. P. Munari, and M. M. Alencar. "Genetic parameter estimates and principal component analysis of breeding values of reproduction and growth traits in female Canchim cattle." Reproduction, Fertility and Development 25, no. 5 (2013): 775. http://dx.doi.org/10.1071/rd12132.
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Phenotypic data from female Canchim beef cattle were used to obtain estimates of genetic parameters for reproduction and growth traits using a linear animal mixed model. In addition, relationships among animal estimated breeding values (EBVs) for these traits were explored using principal component analysis. The traits studied in female Canchim cattle were age at first calving (AFC), age at second calving (ASC), calving interval (CI), and bodyweight at 420 days of age (BW420). The heritability estimates for AFC, ASC, CI and BW420 were 0.03 ± 0.01, 0.07 ± 0.01, 0.06 ± 0.02, and 0.24 ± 0.02, respectively. The genetic correlations for AFC with ASC, AFC with CI, AFC with BW420, ASC with CI, ASC with BW420, and CI with BW420 were 0.87 ± 0.07, 0.23 ± 0.02, –0.15 ± 0.01, 0.67 ± 0.13, –0.07 ± 0.13, and 0.02 ± 0.14, respectively. Standardised EBVs for AFC, ASC and CI exhibited a high association with the first principal component, whereas the standardised EBV for BW420 was closely associated with the second principal component. The heritability estimates for AFC, ASC and CI suggest that these traits would respond slowly to selection. However, selection response could be enhanced by constructing selection indices based on the principal components.
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Konkruea, Tawirat, Skorn Koonawootrittriron, Mauricio A. Elzo, and Thanathip Suwanasopee. "Accuracy of Genomic-Polygenic and Polygenic Breeding Values for Age at First Calving and Milk Yield in Thai Multibreed Dairy Cattle." Annals of Animal Science 19, no. 3 (July 1, 2019): 633–45. http://dx.doi.org/10.2478/aoas-2019-0032.
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AbstractSingle-nucleotide polymorphisms (SNPs) have been used in genomic prediction and shown to increase prediction accuracy and selection responses for economic traits in dairy cattle. The successful report in genomic prediction for improving age at first calving (AFC) and 305-d milk yield (MY) in multibreed dairy population is limited. Therefore, the objective of this research was to compare estimates of variance components, genetic parameters, and prediction accuracies for AFC and MY using a genomic-polygenic model (GPM) and a polygenic model (PM). The AFC and MY records of 9,106 first-lactating multibreed dairy cows, calved between 1991 and 2014, were collected from 1,012 Thai dairy farms. The SNP genotyped individuals were selected from cows that had completed pedigree and phenotypes information. The total genomic DNA samples of 2,661 dairy cattle were genotyped using various GeneSeek Genomic Profiler low-density bead chips (9K, 20K, and 80K). The 2-trait GPM and PM contained herd-year-season and heterosis as fixed effects, and animal additive genetic and residual as random effects. Variance components and genetic parameters were estimated using the procedure of average information-restricted maximum likelihood (AI-REML). Estimates of additive genetic variance components and heritabilities from GPM were higher than PM for AFC and MY. Correlations between AFC and MY were near zero for both models. Mean EBV accuracies were higher for GPM (32.95% for AFC and 38.24% for MY) than for PM (32.65% for AFC, and 32.99% for MY). Mean sire EBV accuracies were higher for GPM (31.35% for AFC and 36.25% for MY) than for PM (28.37% for AFC and 28.80% for MY). Thus, the GPM should be considered the model of choice to increase accuracy of genetic predictions for AFC and MY in the Thai multibreed dairy population.
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Ribeiro, Anamaria Cândido, Alan Jackson McAllister, and Sandra Aidar de Queiroz. "Profitability measures of dairy cows." Revista Brasileira de Zootecnia 37, no. 9 (September 2008): 1607–16. http://dx.doi.org/10.1590/s1516-35982008000900012.
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This study was aimed at defining profitability measures designed for prediction of breeding values (EBV) in dairy cows. Performance and economic data recorded in herds enrolled in the DHIA (Dairy Herd Improvement Association) program in Kentucky, USA, were used to evaluate economic functions which included the following profitability measures: lifetime net income (LNI), efficiency (EF), milk income over feed costs (IOFC), net income per day of productive life (NIPL), net income at the end of the first lactation (NI1), and milk income over feed costs at the end of the first lactation (IOFC1). The estimated averages for LNI, EF, IOFC, NIPL, NI1 and IOFC1 were respectively US$ 532.13, 1.04, US$ 3038.19, US$ -0.16, US$ -69.34 and US$ 1293.77. The heritability estimates for these traits ranged from 0.06 to 0.09. The EBV and Spearman correlation estimates were positive, ranging from moderate to high values, suggesting a direct linear relationship among the profitability measures. LNI was the best profitability measure and genetic correlation estimates between LNI and economic measures recorded in first lactation (NI1 and IOFC1) were moderate (<0.56). NI1 was the most efficient profitability measure, but it would be easier to record data to calculate IOFC1. Overall, results do not suggest any economic function measured in the first lactation as a selection criteria for LNI. The profitability measures were affected by the short productive life of the animals in the herds. Selection based on different profitability measures would not result in similar ranking of sires.
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Leitch, H. W., C. Smith, E. B. Burnside, and M. Quinton. "Effects of female reproductive rate and mating design on genetic response and inbreeding in closed nucleus dairy herds." Animal Science 60, no. 3 (June 1995): 389–400. http://dx.doi.org/10.1017/s1357729800013266.
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AbstractHierarchical (each dam mated to one sire) and factorial (each dam mated to several sires) designs involving juvenile selection in a closed nucleus breeding programme were compared for rates of genetic response and inbreeding using stochastic simulation. Numbers of sires and dams selected and herd sizes varied. Generations were discrete. Sires and dams were selected at 15 months on the basis of an estimated breeding value (EBV) calculated using selection index which considered information on close relatives. Selection was for total merit index. Matings were carried out assuming use of multiple emulation and embryo transfer (MOET) or in vitro embryo production (1VEP) technologies, over a range of reproductive parameters. Reproductive rates assumed a fixed number of potential offspring per collection with IVEP and MOET. Comparison of mating designs using MOET showed that rates of genetic response and inbreeding with factorial designs voere from 88 to 431% and 36 to 111% of those with the hierarchical design. Generally rates of genetic response were increased and inbreeding decreased by increasing the number of mates per dam due to a reduction of correlations among EBV. Reduced rates of genetic response were occasionally observed in factorial designs involving the mating of dams to large numbers of sires. This increased the generation interval due to the time to carry out the matings. Factorial designs were found to be most efficient for increasing genetic response and or decreasing inbreeding, for breeding programmes involving the selection of equal numbers of sires and dam. For the breeding programmes considered, rates of genetic response with IVEP equalled the best of the MOET designs, achieved at highest MOET rates, at the lowest level of IVEP. But at the equivalent rate of genetic response, rate of inbreeding was increased by 8%. The increased rate of inbreeding was due to the shorter generation interval with IVEP, and the increased probability of selecting related individuals assuming all donors respond to IVEP.